They have risen 35 percent since December, but Longbow Research analyst Alton Stump said they are approaching his target price of $38 so he downgraded them to "Neutral" from "Buy."

In a note to clients, he wrote that "we cannot justify recommending investors put additional money into the shares at this time."

Still, he said sales at Whole Foods stores that have been open at least a year seem to be rising, thanks to heavier customer traffic, better economic conditions and increased discounting. The figure is considered a key measure for retailers because it is not skewed by results from stores that opened or closed during the year.

Shares of the company, based in Austin, Texas, have ranged between $16.13 and $37.10 over the past 52 weeks.